BioC 2.13: CHECK report for graph on zin1

Package: graph

Version: 1.40.1

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings graph_1.40.1.tar.gz

StartedAt: 2014-04-05 01:43:03 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:44:11 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 67.5 seconds

RetCode: 0

Status:  OK

CheckDir: graph.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/graph.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.40.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘graph’ can be installed ... [4s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GraphClass.Rnw’, ‘MultiGraphClass.Rnw’, ‘clusterGraph.Rnw’,
  ‘graph.Rnw’, ‘graphAttributes.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘graph_unit_tests.R’ [15s/15s]
 [15s/15s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/graph.Rcheck/00check.log’
for details.

* installing *source* package ‘graph’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c graph.c -o graph.o
gcc -std=gnu99 -shared -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
mv graph.so BioC_graph.so
installing to /home/biocbuild/bbs-2.13-bioc/meat/graph.Rcheck/graph/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (graph)

name	user	system	elapsed
DFS	0.032	0.000	0.033
IMCA	0.168	0.004	0.173
MAPKsig	0.116	0.000	0.117
MultiGraph-class	0.096	0.004	0.103
acc-methods	0.016	0.000	0.016
addEdge	0.064	0.000	0.064
addNode	0.016	0.000	0.017
adj-methods	0.008	0.000	0.007
apoptosisGraph	0.032	0.000	0.029
attrData-class	0.008	0.000	0.011
aveNumEdges	0.012	0.000	0.012
biocRepos	0.004	0.000	0.005
boundary	0.008	0.000	0.009
calcProb	0.004	0.000	0.002
calcSumProb	0.008	0.000	0.010
clearNode	0.016	0.000	0.017
clusterGraph-class	0.008	0.000	0.008
clusteringCoefficient-methods	0.012	0.000	0.011
combineNodes	0.040	0.000	0.039
distGraph-class	0.008	0.000	0.007
duplicatedEdges	0.052	0.000	0.052
edgeMatrix	0.016	0.004	0.019
edgeSets	0.04	0.00	0.04
edgeWeights	0.012	0.004	0.016
fromGXL-methods	0.312	0.000	0.309
graph-class	0.020	0.000	0.022
graph2SparseM	0.172	0.012	0.183
graphAM-class	0.024	0.000	0.024
graphBAM-class	0.064	0.000	0.064
graphExamples	0.008	0.000	0.009
graphNEL-class	0.016	0.000	0.013
inEdges	0.008	0.000	0.007
leaves	0.020	0.000	0.018
listEdges	0.012	0.000	0.013
matrix2Graph	0.108	0.000	0.107
mostEdges	0.024	0.000	0.024
numNoEdges	0.008	0.000	0.007
pancrCaIni	0.116	0.008	0.123
randomEGraph	0.012	0.000	0.011
randomGraph	0.012	0.000	0.011
randomNodeGraph	0.008	0.000	0.008
removeEdge	0.016	0.000	0.014
removeNode	0.008	0.000	0.007
renderInfo-class	0.016	0.000	0.015
reverseEdgeDirections	0.012	0.000	0.010
simpleEdge-class	0.004	0.000	0.005
standardLabeling	0.076	0.000	0.076
subGraph	0.008	0.000	0.006
toDotR-methods	0.032	0.000	0.031
ugraph	0.012	0.000	0.013
validGraph	0.008	0.000	0.006